Reference SNP(refSNP) Cluster Report: rs3794997

Reference SNP(refSNP) Cluster Report: rs3794997

refSNP ID: rs3794997
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	107/129
Map to Genome Build:	36.3

Allele
Variation Class:	SNP: single nucleotide polymorphism
RefSNP Alleles:	A/T
Ancestral Allele:	A
Clinical Association:	unknown

HGVS Names
NM_005968.3:c.439-321A>T
NM_031203.2:c.439-321A>T
NT_077812.2:g.1133883A>T

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss44155519 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs3794997 during BLAST analysis for the current build.

NCBI Assay ID	Handle\|Submitter ID	ss to rs Orientation /Strand	Alleles	5' Near Seq 30 bp	3' Near Seq 30 bp	Entry Date	Update Date	Build Added	Molecule Type	Success Rate
ss4981372	YUSUKE\|IMS-JST152707	fwd/T	A/T	tagtaagattcagctataccaagcccatga	gctctaatttcagtctggcggttctacatt	08/12/02	10/10/03	107	Genomic	unknown
ss16805748	CSHL-HAPMAP\|CSHL-HuAA-200402.chr19.NT_077812.2_1133883	fwd/T	A/T	tagtaagattcagctataccaagcccatga	gctctaatttcagtctggcggttctacatt	02/17/04	03/04/04	120	Genomic	unknown
ss20070525	CSHL-HAPMAP\|CSHL-HuFF-200402.chr19.NT_077812.2_1133883	fwd/T	A/T	tagtaagattcagctataccaagcccatga	gctctaatttcagtctggcggttctacatt	02/21/04	03/04/04	120	Genomic	unknown
ss21520958	SSAHASNP\|WGSA-200403-chr19.chr19.NT_077812.2_1133883	fwd/T	A/T	tagtaagattcagctataccaagcccatga	gctctaatttcagtctggcggttctacatt	03/20/04	03/20/04	121	Genomic	unknown
ss24061090	PERLEGEN\|afd1597197	fwd/T	A/T	tagtaagattcagctataccaagcccatga	gctctaatttcagtctggcggttctacatt	08/10/04	09/13/04	123	Genomic	unknown
ss44155519	ABI\|hCV26073007	fwd/	A/T	tagtaagattcagctataccaagcccatga	gctctaatttcagtctggcggttctacatt	07/18/05	11/03/06	126	Genomic	unknown
ss90898539	BCMHGSC_JDW\|JWB-1142268	fwd/	A/T	tagtaagattcagctataccaagcccatga	gctctaatttcagtctggcggttctacatt	02/26/08	03/01/08	129	Genomic	unknown

Fasta sequence (Legend)

 GCTTGGTAGG GTCTAAGGTC TCTCATGTGT TATGATGTCT TTTTTAGTGC TGATGGTGGT
 AATTGACAGG ACAGAGAGTT GAAGAAGAGA GTCAGTACAG AGCTTCACAG ACCTTCCCAG
 ATGTTGTTTT ACTGCGCAGC CCTCACACAC ACGCCTCCAA CACCTGAAGG ACTTGAAGGA
 TGGGGGCGCT TGTGTGGTCT AGAACTGTTT CTCAAACTTC TGGAAGCCAT TGACGGGGTT
 TGCAGAAGTT ACAAAACCCC ATTGATGAAT TAGTAAGATT CAGCTATACC AAGCCCATGA
 W
 GCTCTAATTT CAGTCTGGCG GTTCTACATT ATATCAGCTA ATCATGTTTC CCTCCCTACC
 CTGCTTTTCT TTTTTACTTA GTGCAATTGA GAGCTGTGTT TTTAGTGCTA CACTTCATGC
 CTTTTCTTCC TTTCCTATTT CTTTAGCTGG ACTCTTCTAA GCTGGTAGTT GAGTTCATTT
 GACTTTCTTG TTAATAGATT TGAGAGATGC TTTCCAAACA ACCTTTCAGT TTCTAAGTCT
 TGAGAATATC ATTTACTGTG CAAGCATGGT TTGCGTTGTA CTGGGTCAGT TAAACGTAAC

GeneView

GeneView via analysis of contig annotation: HNRNPM heterogeneous nuclear ribonucleoprotein M

View variations for gene:

Include clinically associated:

in gene region cSNP has frequency double hit

Group
Label

Contig->mRNA

Gene Model (contig mRNA transcript) Color Legend

reference

NT_077812->NM_005968

function

reference

NT_077812->NM_031203

function

Group label	Contig-->mRNA-->Protein	Contig position	mRNA orientation	Function


reference	NT_077812->NM_005968->NP_005959	1133883	forward	intron

reference	NT_077812->NM_031203->NP_112480	1133883	forward	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs3794997 maps exactly once on NCBI human chromosome 19

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
19	NW_001838480.2	161264	8185345	minus	T	alt_assembly_8	HuRef	HuRef	view	300
19	NW_927173.1	7646295	8387571	plus	A	alt_assembly_1	Celera	Celera	view	300
19	NT_077812.2	1133883	8435887	plus	A	ref_assembly	reference	reference	view	300

NCBI Resource Links

Submitter-Referenced
GenBank
NT_077812

dbSNP Blast Analysis

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/A	A/T	T/T	HWP	A	T
ss24061090	AFD_EUR_PANEL	European	48	IG	0.458	0.375	0.167	0.403	0.646	0.354

	AFD_AFR_PANEL	African American	46	IG	0.870	0.130		0.752	0.935	0.065

	AFD_CHN_PANEL	Asian	48	IG	0.333	0.333	0.333	0.150	0.500	0.500

ss44155519	HapMap-CEU	European	120	IG	0.450	0.450	0.100	1.000	0.675	0.325

	HapMap-HCB	Asian	90	IG	0.178	0.556	0.267	0.439	0.456	0.544

	HapMap-JPT	Asian	88	IG	0.455	0.341	0.205	0.100	0.625	0.375

	HapMap-YRI	Sub-Saharan African	118	IG	1.000				1.000

ss4981372	JBIC-allele		1476	AF					0.537	0.463

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.417+/-0.186	332	260	9	0

Validation Summary:

Validation status

Marker displays
Mendelian segregation

PCR results confirmed
in multiple reactions

Homozygotes detected
in individual genotype data

DoubleHit found by: BCM_SSAHASNP

UNKNOWN

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Revised: May 25, 2006 1:38 PM .